Food insecurity (FI) and water insecurity (WI) are linked with HIV vulnerabilities, yet how these resource insecurities shape HIV prevention needs is understudied. We assessed associations between FI and WI and HIV vulnerabilities among urban refugee youth aged 16–24 in Kampala, Uganda through individual in-depth interviews (IDI) (n = 24), focus groups (n = 4), and a cross-sectional survey (n = 340) with refugee youth, and IDI with key informants (n = 15). Quantitative data was analysed via multivariable logistic and linear regression to assess associations between FI and WI with: reduced pandemic sexual and reproductive health (SRH) access; past 3-month transactional sex (TS); unplanned pandemic pregnancy; condom self-efficacy; and sexual relationship power (SRP). We applied thematic analytic approaches to qualitative data. Among survey participants, FI and WI were commonplace (65% and 47%, respectively) and significantly associated with: reduced SRH access (WI: adjusted odds ratio [aOR]: 1.92, 95% confidence interval [CI]: 1.19–3.08; FI: aOR: 2.31. 95%CI: 1.36–3.93), unplanned pregnancy (WI: aOR: 2.77, 95%CI: 1.24–6.17; FI: aOR: 2.62, 95%CI: 1.03–6.66), and TS (WI: aOR: 3.09, 95%CI: 1.22–7.89; FI: aOR: 3.51, 95%CI: 1.15–10.73). WI participants reported lower condom self-efficacy (adjusted β= -3.98, 95%CI: -5.41, -2.55) and lower SRP (adjusted β= -2.58, 95%CI= -4.79, -0.37). Thematic analyses revealed: (1) contexts of TS, including survival needs and pandemic impacts; (2) intersectional HIV vulnerabilities; (3) reduced HIV prevention/care access; and (4) water insecurity as a co-occurring socio-economic stressor. Multi-method findings reveal FI and WI are linked with HIV vulnerabilities, underscoring the need for HIV prevention to address co-occurring resource insecurities with refugee youth.