<p>Ocean ecological time series grow more useful with longevity, but practical constraints hinder consistency, and evolving scientific priorities necessitate sampling adjustments. We leveraged 30 years of zooplankton observations (five species, 1993–2024) from the western Antarctic Peninsula to quantify how shifts in sampling intensity, timing, and survey frequency influenced accuracy, precision, and predictability. A 67% decline in sample size aliased a long-term trend in ice krill and increased uncertainty by 47% in log₁₀ space across species. Moving survey dates by two weeks influenced the density of salps, pteropods, and Antarctic krill by 48–83%. The ability to predict krill species density declined 47% in a simulated shift from annual to biennial survey frequency. Reduced spatial resolution and slight changes in timing can be accounted for statistically, but temporal gaps represent a challenge. Autonomous approaches are complementary to (rather than substitutable for) net sampling, necessitating ship operations to maintain valuable zooplankton time series.</p>