diff --git a/NEWS.md b/NEWS.md
index 076e0b9..df14b54 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -39,6 +39,16 @@
   tick: the per-frame metrics computation runs asynchronously and only the
   newest result is applied (latest-wins), with results cached for revisits
 
+### Bug Fixes
+
+- Coupled-mode discovery now reads each component's `SimDir` from its
+  current-run output folder (`output_active` / highest `output_NNNN`) when one
+  exists, instead of the component root. A component folder that also held stale
+  loose `.nc` files from an earlier run made `SimDir` (which walks the whole
+  tree) pick up each variable twice and fail to stitch the overlapping time axes
+  ("Time dimension is not in non-decreasing order"); those leftover files are
+  now ignored. The `.climaviz_cache` location is unchanged
+
 ## v0.1.4 - 2025-11-11
 
 ### New Features
diff --git a/src/coupler.jl b/src/coupler.jl
index b430061..6763ad1 100644
--- a/src/coupler.jl
+++ b/src/coupler.jl
@@ -51,15 +51,40 @@ function _prune_to_1M!(simdir)
     return simdir
 end
 
+# Directory a component's `SimDir` should read. `SimDir` walks the tree with
+# `walkdir`, so if a component folder holds both the current run's
+# `output_active`/`output_NNNN` subfolder *and* stale loose `.nc` files left at
+# the top level from an earlier run, it picks up each variable twice and tries
+# to stitch their overlapping time axes ("Time dimension is not in
+# non-decreasing order"). When an `output_active` symlink (or, failing that, the
+# highest-numbered `output_NNNN`) exists, read from it so only the current run's
+# files are seen; otherwise read the folder itself (components like land/ocean
+# write their diagnostics as loose files with no `output_*` subdir).
+function _resolve_sim_path(component_path)
+    active = joinpath(component_path, "output_active")
+    isdir(active) && return active
+    numbered = filter(readdir(component_path)) do entry
+        startswith(entry, "output_") &&
+            !isnothing(tryparse(Int, last(split(entry, "_")))) &&
+            isdir(joinpath(component_path, entry))
+    end
+    isempty(numbered) && return component_path
+    return joinpath(component_path, maximum(numbered))
+end
+
 """
     discover_components(path)
 
 Scan a ClimaCoupler output directory for component subfolders
 (`clima_atmos`, `clima_land`, `clima_ocean`, `clima_seaice`) and return a
 `Vector` of `(label = "atmos", path = …, simdir = SimDir(…))` NamedTuples for
-every component that contains at least one readable variable. The atmos
-component is pruned to its monthly (`_1M_`) native-grid diagnostics (see
-`_prune_to_1M!`); empty folders (e.g. an inactive ocean) are skipped.
+every component that contains at least one readable variable. Each `SimDir` is
+read from the component's current-run output folder (`output_active` /
+`output_NNNN`) when present, ignoring stale loose `.nc` files left at the
+component root (see `_resolve_sim_path`); `path` stays the component root so the
+`.climaviz_cache` location is stable across runs. The atmos component is pruned
+to its monthly (`_1M_`) native-grid diagnostics (see `_prune_to_1M!`); empty
+folders (e.g. an inactive ocean) are skipped.
 """
 function discover_components(path)
     components = NamedTuple{(:label, :path, :simdir), Tuple{String, String, Any}}[]
@@ -67,7 +92,7 @@ function discover_components(path)
         component_path = joinpath(path, subdir)
         isdir(component_path) || continue
         simdir = try
-            ClimaAnalysis.SimDir(component_path)
+            ClimaAnalysis.SimDir(_resolve_sim_path(component_path))
         catch e
             @warn "ClimaViz: failed to read coupler component" component_path exception = e
             continue
diff --git a/test/test_coupler.jl b/test/test_coupler.jl
index 9400d70..56ba93b 100644
--- a/test/test_coupler.jl
+++ b/test/test_coupler.jl
@@ -38,6 +38,44 @@
         @test ClimaViz.discover_components(mktempdir()) == []
     end
 
+    @testset "_resolve_sim_path" begin
+        # Loose files, no output_* subdir (land/ocean convention): use the
+        # folder itself.
+        loose = mktempdir()
+        touch(joinpath(loose, "gpp_1M_average.nc"))
+        @test ClimaViz._resolve_sim_path(loose) == loose
+
+        # output_active symlink present (current-run pointer): read from it.
+        active = mktempdir()
+        mkpath(joinpath(active, "output_0000"))
+        symlink("output_0000", joinpath(active, "output_active"))
+        @test ClimaViz._resolve_sim_path(active) == joinpath(active, "output_active")
+
+        # No output_active, but numbered run folders: take the highest.
+        numbered = mktempdir()
+        mkpath.(joinpath.(numbered, ("output_0000", "output_0002", "output_0001")))
+        touch(joinpath(numbered, "output_unrelated"))  # non-numbered, ignored
+        @test ClimaViz._resolve_sim_path(numbered) == joinpath(numbered, "output_0002")
+    end
+
+    @testset "discover_components ignores stale top-level files" begin
+        # An atmos folder holding the current run under output_active *and* a
+        # stale variable left loose at the top level: only the current run's
+        # variables should appear (this is what previously caused the
+        # "Time dimension is not in non-decreasing order" stitch error).
+        dir = mktempdir()
+        atmos = joinpath(dir, "clima_atmos")
+        mkpath(joinpath(atmos, "output_0000"))
+        symlink("output_0000", joinpath(atmos, "output_active"))
+        touch(joinpath(atmos, "output_0000", "pr_1M_average.nc"))
+        touch(joinpath(atmos, "stale_1M_average.nc"))  # leftover, must be ignored
+
+        comps = ClimaViz.discover_components(dir)
+        @test [c.label for c in comps] == ["atmos"]
+        @test comps[1].path == atmos  # cache root stays the component folder
+        @test sort(collect(keys(comps[1].simdir.vars))) == ["pr"]
+    end
+
     @testset "_prune_to_1M! prunes variable_paths too" begin
         dir = make_fake_coupler_dir()
         comps = ClimaViz.discover_components(dir)