The consistent use of household water treatment and storage (HWTS) technologies is necessary for human health. However, most HWTS options are designed for typical household use as opposed to emergency contexts, where use is less consistent. To investigate ways to improve the consistency of HWTS use in emergencies, we conducted in-person surveys with 108 households in northern Kenya and comparatively analyzed factors that influenced the use of household filters during a protracted drought. Findings showed that about 50% of respondents used their filter consistently over the course of the study. The main limitation to usability was that none of the filters were well-suited for the indoor living environment of the survey respondents. The factors associated with consistency of use varied by filter design. For one-bucket filters, consistent use was associated with ease of assembly, reported availability of spare parts, and peer approval of HWTS use. For two-bucket filters, consistent use was best explained by the certainty regarding when the filter was functioning or not. We suggest that filter manufacturers should reduce the number of parts to mitigate assembly difficulties and should develop flexible filter designs to improve compatibility across households in terms of space and height requirements. Those disseminating filters during protracted emergencies should conduct user training on the assembly and disassembly of unfamiliar filters and ensure affordable access to necessary replacement parts. Finally, to improve consistency of use of new types of filters, implementers should assess the peer approval of these HTWS options among the target population.