diff --git a/CHANGELOG.md b/CHANGELOG.md
index 10c76509186..1d5165828e0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -34,6 +34,10 @@ For more information about this file see also [Keep a Changelog](http://keepacha
  - Support for inspecting and plotting NetCDF output variables within the notebook workflow.
 - added support for soil temperature, relative humidity, soil moisture, and PPFD downscaling to `met_temporal_downscale.Gaussian_ensemble`
 - The PEcAn uncertainty analysis tutorial ("Demo 2") has been updated and reimplemented as a Quarto notebook at `documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.qmd`. (#3570)
+- Added the shared `input_design` matrix, generated via 
+ `runModule.run.write.configs()`/`generate_joint_ensemble_design()`, that keeps
+  parameter draws and sampled inputs aligned across `run.write.configs()`,
+  `write.ensemble.configs()`(#3535, #3634, #3677).
 
 ### Fixed
 
diff --git a/base/workflow/R/run.write.configs.R b/base/workflow/R/run.write.configs.R
index 18756b45559..31e0a388d29 100644
--- a/base/workflow/R/run.write.configs.R
+++ b/base/workflow/R/run.write.configs.R
@@ -8,7 +8,8 @@
 #'
 #' @param settings a PEcAn settings list
 #' @param ensemble.size number of ensemble runs
-#' @param input_design input indices for samples
+#' @param input_design data frame containing the design matrix describing parameter and input indices, as
+#'   documented in \code{runModule.run.write.configs()}.
 #' @param write should the runs be written to the database?
 #' @param posterior.files Filenames for posteriors for drawing samples for ensemble and sensitivity
 #'    analysis (e.g. post.distns.Rdata, or prior.distns.Rdata)
@@ -28,6 +29,15 @@
 run.write.configs <- function(settings, ensemble.size, input_design, write = TRUE,
                               posterior.files = rep(NA, length(settings$pfts)),
                               overwrite = TRUE) {
+
+  # Validate that input_design matches ensemble.size
+  if (nrow(input_design) != ensemble.size) {
+    stop(
+      "input_design has ", nrow(input_design), " rows, but ensemble.size is ",
+      ensemble.size, ".The design matrix must have exactly one row for each run."
+    )
+  }
+                              
   ## Skip database connection if settings$database is NULL or write is False
   if (!isTRUE(write) && is.null(settings$database)) {
     PEcAn.logger::logger.info("Not writing this run to database, so database connection skipped")
diff --git a/base/workflow/R/runModule.run.write.configs.R b/base/workflow/R/runModule.run.write.configs.R
index 959cde2549c..ae6ef91a90c 100644
--- a/base/workflow/R/runModule.run.write.configs.R
+++ b/base/workflow/R/runModule.run.write.configs.R
@@ -2,7 +2,14 @@
 #'
 #' @param settings a PEcAn Settings or MultiSettings object
 #' @param overwrite logical: Replace config files if they already exist?
-#' @param input_design the input indices for samples
+#' @param input_design data.frame design matrix linking parameter draws and any
+#'   sampled inputs across runs. Include a `param` column whose values select
+#'   rows from `trait.samples`/`ensemble.samples` plus optional columns named for
+#'   `settings$run$inputs` tags (e.g. `met`, `soil`) with index (i.e., row number)
+#'   into each input's `path` list. Provide at least one row per planned run
+#'   (median + all SA members and/or `ensemble.size`). Usually generated by
+#'   `generate_joint_ensemble_design()` but custom designs may be supplied.
+#'  If NULL, `generate_joint_ensemble_design()` will be called internally.
 #' @return A modified settings object, invisibly
 #' @importFrom dplyr %>%
 #' @export
@@ -24,6 +31,13 @@ runModule.run.write.configs <- function(settings,
       )
       input_design <- design_result$X
     }
+
+    # Validate design matrix size for MultiSettings
+    if (!is.null(settings$ensemble$size) && nrow(input_design) != settings$ensemble$size) {
+      PEcAn.logger::logger.severe("Input_design has", nrow(input_design), "rows but settings$ensemble$size is",
+           settings$ensemble$size, ". Design matrix must have exactly one row per run.")
+    }
+
     return(PEcAn.settings::papply(settings,
                                   runModule.run.write.configs,
                                   overwrite = FALSE,
@@ -41,6 +55,13 @@ runModule.run.write.configs <- function(settings,
       )
       input_design <- design_result$X
     }
+
+    # Validate design matrix size for Settings
+    if (!is.null(settings$ensemble$size) && nrow(input_design) != settings$ensemble$size) {
+      PEcAn.logger::logger.severe("Input_design has", nrow(input_design), "rows but settings$ensemble$size is",
+           settings$ensemble$size, ". Design matrix must have exactly one row per run.")
+    }
+
     ensemble_size <- nrow(input_design)
 
 
diff --git a/base/workflow/man/run.write.configs.Rd b/base/workflow/man/run.write.configs.Rd
index 84a33d2596c..e53c6924db0 100644
--- a/base/workflow/man/run.write.configs.Rd
+++ b/base/workflow/man/run.write.configs.Rd
@@ -18,7 +18,8 @@ run.write.configs(
 
 \item{ensemble.size}{number of ensemble runs}
 
-\item{input_design}{input indices for samples}
+\item{input_design}{data frame containing the design matrix describing parameter and input indices, as
+documented in \code{runModule.run.write.configs()}.}
 
 \item{write}{should the runs be written to the database?}
 
diff --git a/base/workflow/man/runModule.run.write.configs.Rd b/base/workflow/man/runModule.run.write.configs.Rd
index 9b3341d67c6..3ab40fc4b2c 100644
--- a/base/workflow/man/runModule.run.write.configs.Rd
+++ b/base/workflow/man/runModule.run.write.configs.Rd
@@ -11,7 +11,14 @@ runModule.run.write.configs(settings, overwrite = TRUE, input_design = NULL)
 
 \item{overwrite}{logical: Replace config files if they already exist?}
 
-\item{input_design}{the input indices for samples}
+\item{input_design}{data.frame design matrix linking parameter draws and any
+ sampled inputs across runs. Include a `param` column whose values select
+ rows from `trait.samples`/`ensemble.samples` plus optional columns named for
+ `settings$run$inputs` tags (e.g. `met`, `soil`) with index (i.e., row number)
+ into each input's `path` list. Provide at least one row per planned run
+ (median + all SA members and/or `ensemble.size`). Usually generated by
+ `generate_joint_ensemble_design()` but custom designs may be supplied.
+If NULL, `generate_joint_ensemble_design()` will be called internally.}
 }
 \value{
 A modified settings object, invisibly
diff --git a/book_source/03_topical_pages/03_pecan_xml.Rmd b/book_source/03_topical_pages/03_pecan_xml.Rmd
index f99455cf365..86a94c321e4 100644
--- a/book_source/03_topical_pages/03_pecan_xml.Rmd
+++ b/book_source/03_topical_pages/03_pecan_xml.Rmd
@@ -636,6 +636,35 @@ This information is currently used by the following PEcAn workflow functions:
 - `PEcAn.<MODEL>::write.configs.<MODEL>` -- See [above](#pecan-write-configs)
 - `PEcAn.uncertainty::run.sensitivity.analysis` -- Executes the uncertainty analysis
 
+#### Coordinating inputs with the `input_design` design matrix {#xml-input-design}
+
+Multi-site ensembles that sample over input files use an `input_design`
+data.frame to keep parameter draws and input files aligned across runs. The
+design is created up front (typically via `generate_joint_ensemble_design()`)
+and passed to `runModule.run.write.configs()`. It is not saved automatically to
+`samples.Rdata`, so keep your copy if you need to reuse it.
+
+- **Parameter column:** `param` gives the index (i.e. row number) of the
+posterior draw to use for this run. For example, `param = 5` means use the 5th
+parameter sample from `samples.Rdata`.
+- **Input columns:** any name that matches a tag under `run/inputs` (for
+example `met`, `soil`, `veg`, `poolinitcond`). Values are indices into that
+input’s `path` list. Leaving a column out keeps that input fixed across runs.
+- **Row count and order:** must include exactly one row per run. For ensembles 
+  this means `ensemble.size` rows.
+
+Example layout (CSV or `data.frame`):
+
+| param | met | soil |
+|------:|----:|-----:|
+| 1 | 1 | 1 |
+| 2 | 2 | 1 |
+| 3 | 1 | 2 |
+| 4 | 2 | 2 |
+
+In this example, run 2 would reuse the second parameter draw and also switch to
+the second met driver while keeping the first soil file.
+
 ### Parameter Data Assimilation {#xml-parameter-data-assimilation}
 
 The following tags can be used for parameter data assimilation. More detailed information can be found here: [Parameter Data Assimilation Documentation](#pda)
diff --git a/modules/uncertainty/R/ensemble.R b/modules/uncertainty/R/ensemble.R
index b2807eef320..6863135ea32 100644
--- a/modules/uncertainty/R/ensemble.R
+++ b/modules/uncertainty/R/ensemble.R
@@ -193,7 +193,11 @@ get.ensemble.samples <- function( ensemble.size, pft.samples, env.samples,
 ##' Given a pft.xml object, a list of lists as supplied by get.sa.samples, 
 ##' a name to distinguish the output files, and the directory to place the files.
 ##'
-##' @param input_design the input indices for samples 
+##' @param input_design design matrix describing sampled inputs (see
+##'   `run.write.configs()`). Columns named after `settings$run$inputs` tags give
+##'   1-based indices into each input's `path` list and rows follow run order.
+##'   Requires `nrow(input_design) >= ensemble.size`;
+##'   extra rows are ignored.
 ##' @param ensemble.size size of ensemble
 ##' @param defaults pft
 ##' @param ensemble.samples list of lists supplied by \link{get.ensemble.samples}
diff --git a/modules/uncertainty/man/write.ensemble.configs.Rd b/modules/uncertainty/man/write.ensemble.configs.Rd
index 0545b691418..34decd212ce 100644
--- a/modules/uncertainty/man/write.ensemble.configs.Rd
+++ b/modules/uncertainty/man/write.ensemble.configs.Rd
@@ -18,7 +18,11 @@ write.ensemble.configs(
 )
 }
 \arguments{
-\item{input_design}{the input indices for samples}
+\item{input_design}{design matrix describing sampled inputs (see
+`run.write.configs()`). Columns named after `settings$run$inputs` tags give
+1-based indices into each input's `path` list and rows follow run order.
+Requires `nrow(input_design) >= ensemble.size`;
+extra rows are ignored.}
 
 \item{ensemble.size}{size of ensemble}