The problem isn't as bad with a smaller example (though the runtime is doubled). I've attached a minimum working example, which seems to suggest that maybe there was a problem with xarray creating a MultiIndex and duplicating all the data? (I've left in input() to allow checking memory usage before the program exists, but there isn't much difference in this example). xrmin.py.txt

Edit by @shoyer: added code from attachment inline: ```python

!/usr/bin/env python3

import time import sys import numpy as np import xarray as xr

ds = xr.Dataset() ds['data1'] = xr.DataArray(np.arange(1000), coords={'t1': np.linspace(0, 1, 1000)}) ds['data1b'] = xr.DataArray(np.arange(1000, 2000), coords={'t1': np.linspace(0, 1, 1000)}) ds['data2'] = xr.DataArray(np.arange(2000, 5000), coords={'t2': np.linspace(0, 1, 3000)}) ds['data2b'] = xr.DataArray(np.arange(6000, 9000), coords={'t2': np.linspace(0, 1, 3000)}) if sys.argv[1] == "nodrop": now = time.time() print(ds.where(ds.data1 < 50, drop=True)) print("Took {} seconds".format(time.time() - now)) elif sys.argv[1] == "drop": ds1 = ds.drop('t2') now = time.time() print(ds1.where(ds1.data1 < 50, drop=True)) print("Took {} seconds".format(time.time() - now)) input("Press return to exit") ```