In artisanal small-scale gold mines (ASGM), mercury (Hg) is known to pollute nearby river waters and sediments where it can be methylated to the highly bioavailable methylmercury (MeHg). The assessment of Hg speciation in water samples has been challenging for many years, with recommended procedures often not adequately allowing for analysis of samples in a suitable timeframe. Using a novel solid-phase extraction (SPE) method for sampling and preservation of Hg species, representative speciation data can be safely and easily collected and retained for up to 4-weeks (MeHg = 115 ± 8% refrigerated and 109 ± 13% unrefrigerated storage; Hg2+ = 100 ± 14% refrigerated and 94 ± 12% unrefrigerated storage). Concentrations of MeHg in environmental water samples and drinking water were below detection limit across two ASGM sites in western Kenya and concentrations of Hg2+ were below drinking water guidelines; however, drinking water sources contribute 20–30% of the tolerable weekly intake of Hg, indicating a need to minimise exposure of Hg from dietary sources to prevent Hg poisoning. Sediments from receiving rivers at ASGM sites showed total Hg concentrations above guideline limits (0.08–1.84 mg kg−1 total Hg) along the length of the river; however, MeHg concentrations fluctuated dependent on the stagnation of the river due to damns and ponds (5.9 ± 14.3 µg kg−1 MeHg). The findings show that SPE can be used as a robust sample collection and preservation approach for Hg speciation, which can better inform mitigation measures, understand ecological and human health implications, and improve environmental monitoring.