Surface water from springs, rivers, and dams is often used as an unconventional drinking water source in rural areas where potable water is often unavailable. However, this practice carries significant health risks due to potential contaminants. In this study, the concentrations of arsenic (As) and chromium (Cr) were assessed seasonally using graphite furnace atomic absorption spectrometry (GFAAS). Highly dispersed Fe3O4 nanoparticles were synthesized, characterized, and utilized as adsorbents to remove As and Cr ions from various water matrices. The removal process was optimized by adjusting the mass of the nanoparticles, pH levels, and sonication time. To further understand the adsorption process, adsorption isotherms and kinetics were conducted. Physicochemical properties such as pH, electrical conductivity, and total dissolved solids were seasonally evaluated. The average As concentrations were in the range of 13.3–46.8 µg/L, while Cr was in the range of 1.02–5.04 µg/L. Expectedly, higher concentrations of As and Cr were observed in summer when there was intense precipitation, and the lowest concentrations were observed in winter, with little to no precipitation. The calibrated GFAAS displayed an excellent limit of detection, limit of quantification, and linearity of 0.092–0.13, 0.27–0.34, and 0.27–70 µg/L for As, while 0.031–0.07, 0.16–0.21, and 0.16–70 µg/L were attained for Cr, respectively. Arsenic levels exceeded 10 µg/L in all seasons, indicating that these concentrations were above the maximum permitted levels set by the World Health Organization and the South African National Standards. According to the health risk assessment, high As concentrations were alarming, as they were seasonally increasing, with the chronic daily intake exceeding the oral reference dose, whilst the incremental lifetime cancer risk was significantly high.