This study examined two-year changes in patterns of activity and associations with body mass index (BMI) and waist circumference (WC) among adolescents. Inclinometers (activPAL) assessed sitting, sitting bouts, standing, stepping, and breaks from sitting. ActiGraph-accelerometers assessed sedentary time (SED), light-intensity physical activity (LIPA, stratified as low- and high-LIPA), and moderate-to-vigorous physical activity (MVPA). Anthropometric measures were objectively assessed at baseline and self-reported at follow-up. Data from 324 and 67 participants were obtained at baseline and follow-up, respectively. Multilevel mixed-effects linear regression models examined changes over time, and associations between baseline values and BMI and WC at follow-up. There were significant increases in BMI (0.6 kg/m²) and durations of prolonged sitting (26.4 min/day) and SED (52 min/day), and significant decreases in stepping (-19 min/day), LIPA (-33 min/day), low-LIPA (-26 min/day), high-LIPA (-6.3 min/day), MVPA (-19 min/day), and the number of breaks/day (-8). High baseline sitting time was associated ( = 0.086) with higher BMI at follow-up. There were no significant associations between baseline sitting, prolonged sitting, LIPA, or MVPA with WC. Although changes in daily activity patterns were not in a favourable direction, there were no clear associations with BMI or WC. Research with larger sample sizes and more time points is needed.