1. We sampled Lake Bourget (surface area = 44 km²) using CEN standard gillnet and provisional standard acoustic survey methods over 3 years (2005, 2010 and 2011) as the fish community responded to re-oligotrophication. A total of 16 species were caught in benthic gillnets and three species in pelagic gillnets.

2. Lake Bourget results were consistent with a recent study (Emmrich et al., Freshwater Biology, 57, 2012, 2436) showing strong correspondence between average biomass-per-unit-effort (BPUE) in standard benthic gillnets and average acoustic volume backscattering when smaller lakes (0.25–5.45 km²) were treated as sample units.

3. The BPUE of whitefish (Coregonus lavaretus), perch (Perca fluviatilis) and roach (Rutilus rutilus) measured by benthic gillnets all declined significantly with increasing bathymetric depth; 93% of nets set at depths >50 m caught zero fish.

4. Pelagic gillnetting indicated that small (<10 cm) perch and small (<12.5 cm) roach occupied the upper pelagic habitat (0–20 m depths) and that whitefish were predominant in deeper pelagic habitat. The acoustic sampling showed fish biomass in the upper pelagic habitat varied significantly by year. Biomass there was highest in 2010 when a strong perch year-class recruited and lowest in 2011 when recruitment levels of perch and roach were both weak. Whitefish biomass in deep pelagic habitat (>20 m) increased significantly after 2005.

5. Both surveys showed whitefish biomass increased significantly during the study, but whitefish ≥25 cm were poorly represented in benthic gillnet catches. Contrary to the acoustic findings, the BPUE of perch and roach in benthic gillnets did not vary significantly over time. This metric is insensitive to changes in size structure in that a high catch of small fish and a low catch of large fish in different years can provide similar average BPUE estimates.

6. We examined correlations between BPUE in benthic gillnets and acoustic methods at fine spatial scales by averaging acoustic backscattering measurements encompassed by buffers of varying size (250–2000 m) around individual gillnets and by averaging samples collected from lake quadrants. Correlations at fines scales were generally poor, and only in 1 year was the quadrant correlation significant. The lack of correlation can be explained, in part, by the two gears sampling different components of the fish community. Conversely, in pelagic habitat, where the fish community was simpler, we found BPUE in pelagic nets to be strongly correlated with acoustic backscattering.

7. With respect to large lakes like Lake Bourget, we hypothesise that the congruence in average biomass measurements provided by these two survey methods occurs because these different community components are responding similarly to a common driver like lake trophic status (or possibly multiple drivers operating in synergy).