Transparent exopolymer particles (TEPs) are planktonic, organic microgels that are ubiquitous in aqueous environments. Increasing evidence indicates that TEPs play an active role in the process of aquatic biofilm formation. Frequently, TEPs are intensely colonized by bacteria and other microorganisms, thus serving as hot spots of intense microbial activity. We introduce the term “protobiofilm” to refer to TEPs with extensive microbial outgrowth and colonization. Such particles display most of the characteristics of developing biofilm, with the exception of being attached to a surface. In this study, coastal seawater was passed through custom-designed flow cells that enabled direct observation of TEPs and protobiofilm in the feedwater stream by bright-field and epifluorescence microscopy. Additionally, we could follow biofilm development on immersed surfaces inside the flow cells. Within minutes, we observed TEP and protobiofilm patches adhering to these surfaces. By 30 min, confocal laser-scanning microscopy (CLSM) revealed numerous patches of Con A and SYTO 9 staining structures covering the surfaces. Atomic force microscopy showed details of a thin, highly sticky, organic conditioning layer between these patches. Bright-field and epifluorescence microscopy and CLSM showed that biofilm development (observed until 24 h) was profoundly inhibited in flow cells with seawater prefiltered to remove most large TEPs and protobiofilm. We propose a revised paradigm for aquatic biofilm development that emphasizes the critical role of microgel particles such as TEPs and protobiofilm in facilitating this process. Recognition of the role of planktonic microgels in aquatic biofilm formation can have applied importance for the water industry.