AbstractHorizontal patchiness of water quality attributes in lakes substantially influences the ability to accurately determine an average condition of a lake from traditional in situ sampling. Therefore, spatial variability has to be accounted for in monitoring programmes which aim at determining the states and trends of ecosystem attributes. We used five years of Sentinel-2 Multispectral Instrument (MSI) data and conducted spatial analyses of surface chlorophyll a (Chl) concentration to map its variability and provide concrete recommendations for resource managers to design in situ sampling programmes. First, we developed a regional calibration of Chl predictions by C2RCC, an openly available processor for atmospheric corrections and water constituent retrieval, using in situ data from eleven temperate lakes in the central North Island of Aotearoa New Zealand. Using 93 match-up samples, we re-fitted C2RCC’s partitioning of constituent absorption coefficients to achieve an improved prediction accuracy for Chl (r2 = 0.79, root mean square error = 5.4 mg m−3). The new relationship was applied to all cloud-free images for thirteen regional lakes for further spatial analysis. We found that the medians calculated within areas of different sizes around in situ sampling locations may increase or decrease, illustrating an unpredictable uncertainty of the representativeness of any in situ sample. We went on to summarise five years of spatial variability by assessing each pixel for its tendency to be near the lake median Chl, higher (near the upper quartile) or lower (near the lower quartile). This spatiotemporal analysis revealed recurring patchiness that we converted to an indication of the representativeness of any location in the lake useful for the selection of more representative sites for future monitoring programmes.