Many government agencies and other organizations sample natural alpine and subalpine surface waters using varying protocols for sample storage and filtration. Simplification of protocols would be beneficial if it could be shown that sample quality is unaffected. In this study, samples collected from low ionic strength waters in alpine and subalpine lake inlets and outlets in the western United States were used to evaluate (1) effects of refrigerated storage time on the chemistry of unfiltered samples, and (2) differences in sample filtration protocols. No analytes exhibited significant changes when stored less than 48 h. Six analytes (pH, sodium, ammonium, potassium, chloride, sulfate) exhibited statistically significant (but small) changes when storage time exceeded 48 h. Two analytes (calcium, nitrate) were significantly higher when samples were field filtered than when filtered in the laboratory, but the differences were also small. For waters similar to those in this test, unfiltered refrigerated samples may be stored up to 48 h without compromising sample quality. The small differences between field and lab filtration do not justify the expense, training, and contamination risk of field filtration.