The abundance of six tetracycline resistance genes tet(O), tet(Q), tet(W), tet(M), tet(B) and tet(L), were quantified over time in wastewater lagoons at concentrated animal feeding operations (CAFO) to assess how feedlot operation affects resistance genes in downstream surface waters. Eight lagoons at five cattle feedlots in the Midwestern United States were monitored for 6 months. Resistance and 16S-rRNA gene abundances were quantified using real-time PCR, and physicochemical lagoon conditions, tetracycline levels, and other factors (e.g. feedlot size and weather conditions) were monitored over time. Lagoons were sorted according to antibiotic use practice at each site, and designated as ‘no-use’, ‘mixed-use’ or ‘high-use’ for comparison. High-use lagoons had significantly higher detected resistance gene levels (tetR; 2.8 × 106 copies ml−1) relative to no-use lagoons (5.1 × 103 copies ml−1; P < 0.01) and mixed-use lagoons (7.3 × 105 copies ml−1; P = 0.076). Bivariate correlation analysis on pooled data (n = 54) confirmed that tetR level strongly correlated with feedlot area (r = 0.67, P < 0.01) and ‘total’ bacterial 16S-rRNA gene level in each lagoon (r = 0.51, P < 0.01), which are both characteristic of large CAFOs. tet(M) was the most commonly detected gene, both in absolute number and normalized to 16S-rRNA gene level, although tet(O), tet(Q) and tet(W) levels were also high in the mixed and high-use lagoons. Finally, resistance gene levels were highly seasonal with abundances being 10–100 times greater in the autumn versus the summer. Results show that antibiotic use strategy strongly affects both the abundance and seasonal distribution of resistance genes in associated lagoons, which has implications on water quality and feedlot management practices.