diff --git a/kwant/continuum/_common.py b/kwant/continuum/_common.py
index 9b14ef129bb4ae8a12dbf8c80ba5de883e370841..17a0e0570fd9a23a4a79c4693f1c89b4ea199f10 100644
--- a/kwant/continuum/_common.py
+++ b/kwant/continuum/_common.py
@@ -151,8 +151,10 @@ def sympify(expr, locals=None):
     # if ``expr`` is already a ``sympy`` object we may terminate a code path
     if isinstance(expr, tuple(sympy_classes)):
         if locals:
-            warnings.warn('Input expression is already SymPy object: ' +
-                          '"locals" will not be used.', RuntimeWarning)
+            warnings.warn('Input expression is already SymPy object: '
+                          '"locals" will not be used.',
+                          RuntimeWarning,
+                          stacklevel=2)
         return expr
 
     # if ``expr`` is not a "sympy" then we proceed with sympifying process
diff --git a/kwant/linalg/mumps.py b/kwant/linalg/mumps.py
index 397b4cc963bc9f9d593bce12fcd2c41904bc5912..465ef1aa359ab3c88adbf5a4a4ccf125c73094dd 100644
--- a/kwant/linalg/mumps.py
+++ b/kwant/linalg/mumps.py
@@ -299,7 +299,9 @@ class MUMPSContext:
         if reuse_analysis:
             if self.mumps_instance is None:
                 warnings.warn("Missing analysis although reuse_analysis=True. "
-                              "New analysis is performed.", RuntimeWarning)
+                              "New analysis is performed.",
+                              RuntimeWarning,
+                              stacklevel=2)
                 self.analyze(a, ordering=ordering, overwrite_a=overwrite_a)
             else:
                 dtype, row, col, data = _make_assembled_from_coo(a,
diff --git a/kwant/plotter.py b/kwant/plotter.py
index 4c17c8bbc1f06b108e3f3ee17700194e20b0b508..d164dfcfcf3af4cf211c976420f3ecd9c251b273 100644
--- a/kwant/plotter.py
+++ b/kwant/plotter.py
@@ -67,7 +67,7 @@ def matplotlib_chores():
         warnings.warn("Matplotlib 1.4.0 has a bug that makes 3D plotting "
                       "unusable (2D plotting is not affected). Please "
                       "consider using a different version of matplotlib.",
-                      RuntimeWarning)
+                      RuntimeWarning, stacklevel=2)
 
     pre_1_4_matplotlib = [int(x) for x in ver.split('.')[:2]] < [1, 4]
 
@@ -1457,7 +1457,7 @@ def mask_interpolate(coords, values, a=None, method='nearest', oversampling=3):
     if min_dist < 1e-6 * np.linalg.norm(cmax - cmin):
         warnings.warn("Some sites have nearly coinciding positions, "
                       "interpolation may be confusing.",
-                      RuntimeWarning)
+                      RuntimeWarning, stacklevel=2)
 
     if a is None:
         a = min_dist