Background: A current focus of biofilm research is the chemical interaction between microorganisms within the biofilms. Prerequisites for this research are bioassay systems which integrate reliable tools for the planning of experiments with robot-assisted measurements and with rapid data processing. Here, data structures that are both human-and machine readable may be particularly useful. Results: In this report, we present several simplification and robotisation options for an assay of bacteria-induced biofilm formation by the freshwater diatom Achnanthidiumminutissimum. We also tested several proof-of-concept robotisation methods for pipetting, as well as for measuring the biofilm absorbance directly in the multi-well plates. Furthermore, we exemplify the implementation of an improved data processing workflow for this assay using the Konstanz Information Miner (KNIME), a free and open source data analysis environment. The workflow integrates experiment planning files and absorbance read-out data, towards their automated processing for analysis. Conclusions: Our workflow lead to a substantial reduction of the measurement and data processing workload, while still reproducing previously obtained results in the A. minutissimum biofilm assay. The methods, scripts and files we designed are described here, offering adaptable options for other medium-throughput biofilm screenings.