There’s some pleasant waterfront running in the marina/port area of Pisa, which is located ~10 km from the historical centre. The route is nearly 8 km out and back.
Start with a ~2 km loop around the Marina and out to the North Pier. Then, come back to the South Pier and continue south along the waterfront path that runs alongside road for ~2.5 km, past the Piazza Giuseppe Viviani, as far as about Bagno Luisa, where the road turns a bit inland. There are great views of the Ligurian Sea, and several beaches along the way. Retrace your steps back to the Marina.
Alternative Return/Longer Run: Instead of returning along the waterfront, you can join the Ciclopista del Trammino, a paved multi-use path. From the waterfront, access it from Piazza Sardegna, using Via Cagliaritana. The path goes back to the marina are and continues for ~11 km east to central Pisa.