We opportunistically included a chikungunya envelope 1 recombinant virus antigen (CHIKV E1), a dengue 2 virus-like protein (DENV-2 VLP), and a DENV-3 VLP in a multiplex bead assay (MBA) for serological assessment involving improvements in water, sanitation, and hygiene for students attending 42 elementary schools in southern Mali in Western Africa. From students attending grades 1-6,805 dried blood spots (DBS) were collected. Immunoglobulin (Ig) G was eluted from the DBS and was probed for responses to the antigens. For all students, positive IgG responses to CHIKV E1, DENV-2 VLP, and DENV-3 VLP were 6.2%, 24.3%, and 14.8%, respectively. However, in some schools the positivity rate was as high as 21.1% for CHIKV E1 and 66.7% for both DENV-2 and DENV-3 VLP. In one set of schools, cluster analysis from SaTScan software showed a relative risk of 3.1 and 5.1 for DENV-2 and DENV-3 VLP, respectively, compared with schools outside the cluster. The MBA serology platform is very flexible in that additional antigens other than the intended targets can be included with very little cost and can provide additional effective opportunities for evaluation of public health activities.