Many ecological processes in intertidal areas act at very small (mm to cm) spatial scales so manipulative ecological experiments are done at scales at which these processes are proposed to occur. Remote-sensing using field-based sensors enable ecologists to capture variability that must be measured to test hypotheses about small-scale processes. We present two case studies where remote-sensing from field-based platforms has been used to acquire data for manipulative ecological experiments in intertidal areas. The first study, from a rock platform, investigates the spatial scales of variability in chlorophyll (as an index of algal biomass) in experimental plots prior to and after the removal of encrusting macro-algae. Digital colour-infrared (CIR) imagery of the rock platform was obtained before the removal of the encrusting macro-algae and on 1, 44, 75, 117 and 160 days after removal. Amount of chlorophyll was derived from the CIR data using a simple ratio of reflectances at near-infrared (NIR) and red wavelengths. Block Mean Square (BMS) analysis showed that there was little variability in amounts of chlorophyll at very small (= 2.26 cm2) scales, prior to and after removal of encrusting macro-algae. The greatest variability occurred at the largest block-size analysed (36.19 cm2). This identifies the spatial scale at which micro-algal food resources are variably scattered on the shore. Results discriminate variability at about 60–80 mm distances. Distributions of micro-algae are caused by a complicated interplay of scale-dependent ecological processes, including grazing. These findings provide a basis for the design of manipulative experiments at appropriate scales to unravel these processes. The second study used field reflectance spectra (350–1050 nm) to: i) determine whether the amount of algae in soft sediments could be changed by manipulating the amounts of light reaching the sediment surface and ii) test the hypothesis that the strength of in vivo absorption features, as indices of the amount of chlorophyll and other pigments, was correlated with measures of sediment-stability (erosion threshold and erosion rate). Several different measures of the strength of absorption features were investigated to determine the best predictor of stability of the sediment. Reflectance spectra showed that amounts of algae had been successfully manipulated. Derivative reflectance at individual wavelengths, indicative of absorption by chlorophyll-a and chlorophyll-c, were the best predictors of sediment-stability. These case studies demonstrate some novel uses of field-based remote-sensing to provide information at the spatial scales relevant to many intertidal ecologists. Such techniques should have an increasingly important role in ecological field experimentation where non-destructive sampling of photosynthetic pigments is desired.