Results of microbial water quality conducted in Kwale County, Kenya from 2015 to 2017 by University of Oxford and Universitat Politecnica de Catalunya as part of the Gro for GooD project (https://upgro.org/consortium/gro-for-good/). Water samples from 101 locations (including 31 open wells, 27 deep boreholes, 21 shallow boreholes with handpumps, 15 covered dug wells with handpumps, and 10 surface water sites. This data set contains results for microbial risk parameters including Escherichia coli, thermotolerant coliforms (TTCs) and tryptophan-like fluorescence (TLF). Most samples also have accompanying data on pH, conductivity, water temperature and turbidity. Duplicate and replicate samples are included and indicated by 'Dup' or 'Rep'. Duplicates samples were collected from the same water points within minutes of each other and laboratory replicates were different aliquots from a single sample. Risk classifications of E. coli and TTC data are based on the World Health Organisation's microbial water quality risk grading scheme. Manufacturer recommended sampling protocols were used. The sampled water points were in regular use and boreholes were flushed with either an electric pump or hand-pumping prior to sample collection. Samples from the open wells were drawn with buckets and rope, which were designated for each site and were rinsed prior to sampling to minimise secondary contamination. Daily field and laboratory blank samples were analysed to confirm no secondary contamination or cross-contamination between sites. For the tryptophan-like fluorescence (TLF) measurement, approximately three litres of unfiltered water were pumped or poured into a stainless-steel container (kept in a black box to prevent ambient light from interfering). The container was cleaned with ethanol and triple-rinsed with sample water prior to each measurement. Measurement was conducted for approximately 3 minutes and the median result was used. The probe and its sensor window were kept clean. Air bubble formation on the sensor window was avoided. For the bacteria sampling, sterile purpose-made bags were used for sample collection and immediately stored in a cooler box with ice-packs. They were transported and processed to begin incubation within two to five hours. Gro for GooD: Groundwater Risk Management for Growth and Development