There is currently renewed interest in aqueous dye-sensitized solar cells (DSCs). Water ingress in conventional DSCs leads to a loss of efficiency; one solution to this problem is to optimize the cells to work in the presence of water. The aim is to create a stable cell and to avoid the need for buffer layers and encapsulation that increase device cost. Water containing electrolytes generally give lower photocurrents than those based on organic solvents, a problem that has in part been attributed to poor pore filling by the aqueous electrolyte. Here, two sets of cells have been made that are identical except for the nature of the solvent (water or acetonitrile). Photocurrent mapping has been used to compare spatially resolved inhomogeneities in the current density. High-resolution transmission mapping (3906 data points/cm2) has been used to decouple dye coverage and film thickness from electrolyte permeation. Filling cells using heating and vacuum was found to improve water electrolyte permeation. Photocurrent maps suggest that dye desorption occurs adjacent to the filling holes in both acetonitrile- and water-based cells, with significantly more dye desorbed in the water-based cells. The loss of dye was attributed to desorption by the tert-butyl pyridine base in the electrolyte.