The aim of this study was to evaluate heat exposure, dehydration, and kidney function in rice workers over the course of three months, in Guanacaste, Costa Rica. We collected biological and questionnaire data across a three-month-period in male field (n = 27) and other (n = 45) workers from a rice company where chronic kidney disease of unknown origin (CKDu) is endemic. We used stepwise forward regression to determine variables associated with estimated glomerular filtration rate eGFR at enrollment and/or change in eGFR, and Poisson regression to assess associations with incident kidney injury (IKI) over the course of three months. Participants were 20–62 years old (median = 40 in both groups). Dehydration was common (≥37%) in both groups, particularly among other workers at enrollment, but field workers were more exposed to heat and had higher workloads. Low eGFR (<60 mL/min/1.73 m²) was more prevalent in field workers at enrollment (19% vs. 4%) and follow-up (26% vs. 7%). Field workers experienced incident kidney injury (IKI) more frequently than other workers: 26% versus 2%, respectively. Age (β = −0.71, 95%CI: −1.1, −0.4), current position as a field worker (β = −2.75, 95%CI: −6.49, 0.99) and past work in construction (β = 3.8, 95%CI: −0.1, 7.6) were included in the multivariate regression model to explain eGFR at enrollment. The multivariate regression model for decreased in eGFR over three month included current field worker (β = −3.9, 95%CI: −8.2, 0.4), current smoking (β= −6.2, 95%CI: −13.7–1.3), dehydration (USG ≥ 1.025) at both visits (β= −3.19, 95%CI: −7.6, 1.2) and pain medication at follow-up (β= −3.2, 95%CI: −8.2, 1.95). Current fieldwork [IR (incidence rate) = 2.2, 95%CI 1.1, 5.8) and being diabetic (IR = 1.8, 95%CI 0.9, 3.6) were associated with IKI. Low eGFR was common in field workers from a rice company in Guanacaste, and being a field worker was a risk factor for IKI, consistent with the hypothesis that occupational heat exposure is a critical risk factor for CKDu in Mesoamerica.