diff --git a/echopype/calibrate/ek80_complex.py b/echopype/calibrate/ek80_complex.py
index 5c93118b1..8b2dc03dd 100644
--- a/echopype/calibrate/ek80_complex.py
+++ b/echopype/calibrate/ek80_complex.py
@@ -1,4 +1,5 @@
 from collections import defaultdict
+from functools import partial
 from typing import Dict, Literal, Optional, Union
 
 import numpy as np
@@ -226,11 +227,10 @@ def get_transmit_signal(
     # but keeping this here for use as standalone function
     if waveform_mode == "BB" and np.all(beam["transmit_type"] == "CW"):
         raise TypeError("File does not contain BB mode complex samples!")
-
     # Generate all transmit replica
     y_all = {}
     y_time_all = {}
-    # TODO: expand to deal with the case with varying tx param across ping_time
+    # TODO: expand to deal with the case with varying non-NaN tx param across ping_time
     tx_param_names = [
         "transmit_duration_nominal",
         "slope",
@@ -240,16 +240,18 @@ def get_transmit_signal(
     for ch in beam["channel"].values:
         tx_params = {}
         for p in tx_param_names:
-            tx_params[p] = np.unique(beam[p].sel(channel=ch))
+            # Extract beam values and filter out NaNs
+            beam_values = np.unique(beam[p].sel(channel=ch))
+            # Filter out NaN values
+            beam_values_without_nan = beam_values[~np.isnan(beam_values)]
+            tx_params[p] = beam_values_without_nan
             if tx_params[p].size != 1:
                 raise TypeError("File contains changing %s!" % p)
         fs_chan = fs.sel(channel=ch).data if isinstance(fs, xr.DataArray) else fs
         tx_params["fs"] = fs_chan
         y_ch, _ = tapered_chirp(**tx_params)
-
         # Filter and decimate chirp template
         y_ch, y_tmp_time = filter_decimate_chirp(coeff_ch=coeff[ch], y_ch=y_ch, fs=fs_chan)
-
         # Fill into output dict
         y_all[ch] = y_ch
         y_time_all[ch] = y_tmp_time
@@ -257,6 +259,38 @@ def get_transmit_signal(
     return y_all, y_time_all
 
 
+def _nan_check_convolve(m, replica):
+    """
+    Convolve two arrays while handling NaN values efficiently.
+
+    Parameters
+    ----------
+    m : array-like
+        Input array.
+    replica : array-like
+        Array for convolution.
+
+    Returns
+    -------
+    array-like
+        Convolved array.
+
+    Notes
+    -----
+    If all elements in `m` are NaN, the function returns `m`.
+    If any element in `m` is NaN, direct convolution is performed.
+    Otherwise, FFT convolution is used.
+
+    Direct convolution is slower than FFT but works when NaN values are present.
+    """
+    if np.all(np.isnan(m)):
+        return m
+    elif np.any(np.isnan(m)):
+        return signal.convolve(m, replica, mode="full", method="direct")[replica.size - 1 :]
+    else:
+        return signal.convolve(m, replica, mode="full", method="fft")[replica.size - 1 :]
+
+
 def compress_pulse(backscatter: xr.DataArray, chirp: Dict) -> xr.DataArray:
     """Perform pulse compression on the backscatter data.
 
@@ -278,11 +312,18 @@ def compress_pulse(backscatter: xr.DataArray, chirp: Dict) -> xr.DataArray:
         # Select channel `chan` and drop the specific beam dimension if all of the values are nan.
         backscatter_chan = backscatter.sel(channel=chan).dropna(dim="beam", how="all")
 
+        # Extract transmit values
         tx = chirp[str(chan.values)]
+
+        # Compute complex conjugate of transmit values and reverse order of elements
         replica = np.flipud(np.conj(tx))
 
+        # Create partial of nan_check_convolve with passed in replica
+        _nan_check_convolve_partial = partial(_nan_check_convolve, replica=replica)
+
+        # Apply convolve on backscatter (along range sample dimension) and replica
         pc = xr.apply_ufunc(
-            lambda m: (signal.convolve(m, replica, mode="full")[replica.size - 1 :]),
+            _nan_check_convolve_partial,
             backscatter_chan,
             input_core_dims=[["range_sample"]],
             output_core_dims=[["range_sample"]],
diff --git a/echopype/calibrate/env_params.py b/echopype/calibrate/env_params.py
index 49be4d12c..1bab6cabb 100644
--- a/echopype/calibrate/env_params.py
+++ b/echopype/calibrate/env_params.py
@@ -50,9 +50,12 @@ def harmonize_env_param_time(
         if "time1" not in p.coords:
             return p
 
-        # If there's only 1 time1 value,
-        # or if after dropping NaN there's only 1 time1 value
-        if p["time1"].size == 1 or p.dropna(dim="time1").size == 1:
+        # If there's only 1 time1 value:
+        if p["time1"].size == 1:
+            return p.squeeze(dim="time1").drop("time1")
+
+        # If after dropping NaN there's only 1 time1 value:
+        if p.dropna(dim="time1").size == 1:
             return p.dropna(dim="time1").squeeze(dim="time1").drop("time1")
 
         if ping_time is None: