diff --git a/docs/changelog.txt b/docs/changelog.txt
index ff3943a28c..a1cd692d70 100644
--- a/docs/changelog.txt
+++ b/docs/changelog.txt
@@ -62,6 +62,7 @@ Template for new versions:
 ## Fixes
 - Fix broken weather lookup in ``World::ReadCurrentWeather``
 - `timestream`: deal properly with units who have breathing difficulties
+- `aquifer`: make ``--skip-top`` and top-relative ``--levels`` take effect for the ``drain``, ``convert``, and ``add`` actions instead of being silently ignored
 
 ## Misc Improvements
 - Added ``Coord2d`` and ``Coord3d`` C++ templates, providing a standard set operations for 2-tuples and 3-tuples of any numeric type
diff --git a/plugins/aquifer.cpp b/plugins/aquifer.cpp
index ca00689628..98968a9496 100644
--- a/plugins/aquifer.cpp
+++ b/plugins/aquifer.cpp
@@ -151,6 +151,7 @@ static void get_z_range(color_ostream &out, int & minz, int & maxz, const df::co
     else
         maxz = get_max_aq_z(out, pos1, pos2) - skip_top;
 
+    maxz = std::min((int)pos2.z, maxz);
     minz = std::max((int)pos1.z, maxz - levels + 1);
 
     DEBUG(log,out).print("calculated z range: minz={}, maxz={}\n", minz, maxz);
@@ -188,11 +189,32 @@ static void aquifer_list(color_ostream &out, df::coord pos1, df::coord pos2, int
     }
 }
 
+// adjust the pos range to honor --skip-top and top-relative --levels,
+// which are only meaningful when the target is the whole map (--all).
+// for drain/convert the reference level is the topmost existing aquifer;
+// for add it is the topmost level that can hold an aquifer tile.
+static bool apply_top_relative_z(color_ostream &out, df::coord & pos1, df::coord & pos2,
+    int skip_top, int levels, bool top_is_aq)
+{
+    int minz = 0, maxz = -1;
+    get_z_range(out, minz, maxz, pos1, pos2, levels, top_is_aq, skip_top);
+    if (maxz < minz)
+        return false;
+    pos1.z = minz;
+    pos2.z = maxz;
+    return true;
+}
+
 static int aquifer_drain(color_ostream &out, string aq_type,
-    df::coord pos1, df::coord pos2, int skip_top, int levels, bool leaky)
+    df::coord pos1, df::coord pos2, int skip_top, int levels, bool leaky, bool top_relative)
 {
-    DEBUG(log,out).print("entering aquifer_drain: aq_type={}, pos1={}, pos2={}, skip_top={}, levels={}, leaky={}\n",
-        aq_type, pos1, pos2, skip_top, levels, leaky);
+    DEBUG(log,out).print("entering aquifer_drain: aq_type={}, pos1={}, pos2={}, skip_top={}, levels={}, leaky={}, top_relative={}\n",
+        aq_type, pos1, pos2, skip_top, levels, leaky, top_relative);
+
+    if (top_relative && !apply_top_relative_z(out, pos1, pos2, skip_top, levels, true)) {
+        DEBUG(log, out).print("no aquifer levels in range after skip_top/levels\n");
+        return 0;
+    }
 
     const bool all = aq_type == "all";
     const bool heavy_state = aq_type == "heavy";
@@ -211,10 +233,15 @@ static int aquifer_drain(color_ostream &out, string aq_type,
 }
 
 static int aquifer_convert(color_ostream &out, string aq_type,
-    df::coord pos1, df::coord pos2, int skip_top, int levels, bool leaky)
+    df::coord pos1, df::coord pos2, int skip_top, int levels, bool leaky, bool top_relative)
 {
-    DEBUG(log,out).print("entering aquifer_convert: aq_type={}, pos1={}, pos2={}, skip_top={}, levels={}, leaky={}\n",
-        aq_type, pos1, pos2, skip_top, levels, leaky);
+    DEBUG(log,out).print("entering aquifer_convert: aq_type={}, pos1={}, pos2={}, skip_top={}, levels={}, leaky={}, top_relative={}\n",
+        aq_type, pos1, pos2, skip_top, levels, leaky, top_relative);
+
+    if (top_relative && !apply_top_relative_z(out, pos1, pos2, skip_top, levels, true)) {
+        DEBUG(log, out).print("no aquifer levels in range after skip_top/levels\n");
+        return 0;
+    }
 
     const bool heavy_state = aq_type == "heavy";
 
@@ -232,10 +259,15 @@ static int aquifer_convert(color_ostream &out, string aq_type,
 }
 
 static int aquifer_add(color_ostream &out, string aq_type,
-    df::coord pos1, df::coord pos2, int skip_top, int levels, bool leaky)
+    df::coord pos1, df::coord pos2, int skip_top, int levels, bool leaky, bool top_relative)
 {
-    DEBUG(log,out).print("entering aquifer_add: aq_type={}, pos1={}, pos2={}, skip_top={}, levels={}, leaky={}\n",
-        aq_type, pos1, pos2, skip_top, levels, leaky);
+    DEBUG(log,out).print("entering aquifer_add: aq_type={}, pos1={}, pos2={}, skip_top={}, levels={}, leaky={}, top_relative={}\n",
+        aq_type, pos1, pos2, skip_top, levels, leaky, top_relative);
+
+    if (top_relative && !apply_top_relative_z(out, pos1, pos2, skip_top, levels, false)) {
+        DEBUG(log, out).print("no levels in range after skip_top/levels\n");
+        return 0;
+    }
 
     const bool heavy_state = aq_type == "heavy";
 
diff --git a/plugins/lua/aquifer.lua b/plugins/lua/aquifer.lua
index d5255ccd33..d735a380d1 100644
--- a/plugins/lua/aquifer.lua
+++ b/plugins/lua/aquifer.lua
@@ -135,11 +135,11 @@ function parse_commandline(args)
     local modified = 0
 
     if action == 'drain' then
-        modified = aquifer_drain(aq_type or 'all', pos1, pos2, opts.skip_top, opts.levels, opts.leaky)
+        modified = aquifer_drain(aq_type or 'all', pos1, pos2, opts.skip_top, opts.levels, opts.leaky, opts.all)
     elseif action == 'convert' then
-        modified = aquifer_convert(aq_type, pos1, pos2, opts.skip_top, opts.levels, opts.leaky)
+        modified = aquifer_convert(aq_type, pos1, pos2, opts.skip_top, opts.levels, opts.leaky, opts.all)
     elseif action == 'add' then
-        modified = aquifer_add(aq_type, pos1, pos2, opts.skip_top, opts.levels, opts.leaky)
+        modified = aquifer_add(aq_type, pos1, pos2, opts.skip_top, opts.levels, opts.leaky, opts.all)
     else
         qerror(('invalid action: %s'):format(action))
     end