Colloid deposition in unsaturated, nonuniform porous media is poorly explained by current models and difficult to measure using breakthrough curves and retained mass profiles. We present new methods which enable time-lapse fluorescence imaging to quantify variations in pore saturation, θ, and colloid deposition in 2D, nonuniform unsaturated flow fields. Calibration experiments revealed direct proportionality between fluorescence F and θ in 20/30 mesh quartz sand. Analysis of breakthrough data in fluorescence images allows quantification of the mean mobile concentration, mean deposition rate, and hence the colloid removal efficiency η directly from data at the pixel-scale throughout the flow field. We imaged carboxylate-modified latex microspheres from a point source in saturated flow and unsaturated flow across a capillary fringe at 10−3, 10−2, and 10−1 M NaCl. Total numbers of colloids deposited and values of η increased with ionic strength. We modeled the observed variations in η with θ to estimate the partitioning of colloid deposition between air–water and solid–water interfaces. In the broad saturation range 0.2 < θ < 1, our results suggest that only at the lowest ionic strength, where deposition at solid–water interfaces was strongly unfavorable, did colloid deposition associated with air–water interfaces significantly influence the total colloid removal.