This dataset compiles species-resolved cell abundances (cells L⁻¹) of potentially harmful microalgae (PHM) from 29 sampling events, during low tides, across ~260 km of Kenya's shoreline, conducted monthly in Mombasa from August 2021 to July 2022, and twice from other coastal areas (dry/wet monsoons), with supplementary surveys in September 2021, March 2022, and July 2022 for inaccessible sites. Of these events, 24 targeted Mombasa-area creeks (Kilindini and Tudor) and adjacent waters, while 5 covered southern nearshore reef-fringing and oceanic sites (Shimoni, Chale, Mwaepe, Diani, Tiwi), yielding 463 water samples in total. Surface seawater (0–0.5 m) was collected via 20-μm phytoplankton net (20 L filtered to 50 mL, fixed in 5% Lugol's iodine). In situ parameters (temperature, salinity, pH, conductivity, dissolved oxygen, turbidity, GPS coordinates) were recorded using KoboToolbox on smartphones, with associated environmental data published separately (Oduor et al., 2024). At the Kenya Marine and Fisheries Research Institute (KMFRI) Mombasa laboratory, replicates (A–C per station/event) were subsampled (2 mL), settled in Sedgewick-Rafter chambers, and enumerated via inverted light microscopy at 200× magnification following standard protocols (Chrétiennot-Dinet et al., 1993; Lundholm et al., 2009). Taxonomic identification used IOC-UNESCO HAB manuals (Botes, 2003; Hansen et al., 2001) and was verified against the World Register of Marine Species (WoRMS) and AlgaeBase (https://www.algaebase.org/). The data table details taxonomy (class, genus, species), ecological groups (diatoms, dinoflagellates, cyanobacteria, silicoflagellates), and harm categories. Harm categories classify taxa as toxin producers (e.g., Pseudo-nitzschia, Alexandrium, Dinophysis spp.), oxygen depleters (e.g., Skeletonema, Thalassiosira, Rhizosolenia spp.), gill cloggers (e.g., Chaetoceros, Dictyocha spp.; bloom thresholds: ≥10⁴ cells mL⁻¹ physical; ≥500 cells L⁻¹ toxins; (Hallegraeff et al., 2021; Hansen et al., 2001; Lunholm et al., 2009 onwards)), or other HAB risks (Gu et al., 2022; Hansen et al., 2001). Toxin production includes Paralytic Shellfish Toxins (PST), Diarrheic Shellfish Poisoning (DSP), Amnesic Shellfish Poisoning (ASP), Neurotoxic Shellfish Poisoning (NSP), Ciguatera Fish Poisoning (CFP), Hepatotoxic Shellfish Poisoning (HSP), and Azaspiracid Shellfish Poisoning (AZP). These data facilitate biogeographic, ecological, and risk-assessment studies of PHM diversity (e.g., Margalef richness; Magurran, 2004), functional traits, habitat affinities (Mombasa creeks vs. southern sites), and spatiotemporal patterns, integrable with environmental/toxin measurements, to explore physicochemical drivers and phycotoxin risks.

Abundances were calculated per APHA (1995) and Stirling (1985):N=(A×1000×C)/(V×F×L)(Where N= cells L⁻¹, A= cells counted, C= concentrate volume (mL), V= field volume (mm³), F= fields counted, L= filtered volume (L)).