In this experiment, we studied the effect of seaweed farming and trampling on the seagrass community dynamics in the field in Chwaka Bay (Unguja Island, Zanzibar Archipelago, Tanzania). This dataset comprises the cover and shoot density of two seagrass species (Thalassia hemprichii and Halophila stipulacea) and the cover of its associated benthic macroalgae community. In addition, we measured the morphology of Thalassia hemprichii and the temperature, conductivity, pH, dissolved oxygen and light intesnity during the experiment. We delimited three blocks (A, B, and C, separated by approximately 50 m) in an area dominated by T. hemprichii with presence of H. stipulacea and a mixed macroalgae community. We built three treatment plots (each 3 m wide and 4 m long, with an area of 12 m2) nested within each block: one seaweed farm plot, one trampling plot, and one control plot (each separated by 3–5 m within a block), resulting in a total of three replicate plots per treatment. The seaweed farm consisted of four seaweed lines (ropes) tied to eight wooden pegs (two for each line), as is done in the off-bottom farming method. In each of the ropes, twelve E. denticulatum seedlings were attached by using the "tie-tie" method with a total of 48 seedlings per farm. The seedling size was standardized based on typical farming practices for E. denticulatum used at the beginning of the harvesting cycle. The trampling plot consisted of the same line structure as the seaweed farm plot, but without E. denticulatum attached to the ropes. The control plot consisted of four wooden pegs pressed into the sediment within the seagrass meadow, delimiting an area of the same size as the seaweed farm plot. The experiment ran for 96 days (25.11.2015–29.02.2016) and was sampled approximately every 15 days for a total of seven sampling events (Chwaka1: 25/11/2015, Chwaka2: 09/12/2015, Chwaka3: 28/12/2015, Chwaka4: 13/01/2016, Chwaka5: 27/01/2016, Chwaka6: 14/02/2016, and Chwaka7: 29/02/2016).