Photosystem II (PSII) is a multi-subunit enzymatic complex embedded in the thylakoid membranes responsible for the primary photosynthetic reactions vital for plants. Many herbicides used for weed control inhibit PSII by interfering with the photosynthetic electron transport at the level of the D1 protein, through competition with the native plastoquinone for the QB site. Molecular details of the interaction of these herbicides in the D1 QB site remain to be elucidated in plants. Here, we investigated the inhibitory effect on plant PSII of the PSII-inhibiting herbicides diuron, metobromuron, bentazon, terbuthylazine and metribuzin. We combined analysis of OJIP chlorophyll fluorescence kinetics and PSII activity assays performed on thylakoid membranes isolated from pea plants with molecular docking using the high-resolution PSII structure recently solved from the same plant. Both approaches showed for terbuthylazine, metribuzin and diuron the highest affinity for the D1 QB site, with the latter two molecules forming hydrogen bonds with His215. Conversely, they revealed for bentazon the lowest PSII inhibitory effect accompanied by a general lack of specificity for the QB site and for metobromuron an intermediate behavior. These results represent valuable information for future design of more selective herbicides with enhanced QB binding affinities to be effective in reduced amounts.