All sorts of options exist, depending on your affinity for ambience and budget. To name a few:
Koho Bistro at Bailey Hill West of 18th has a nice Seafood Chowder and a menu with a nice variety of Seafood and non-seafood.
McMenamin's North Bank off Coburg Rd / Country Club along the Willamette has nice patio seating in the season and decent microbrews.
Cafe Lucky Noodle has seafood dishes and plays in the Asian / Italian genre. 5th at Oak
Sushi Station 5th at Oak
Steelhead Brewpub 5th at Oak
The Fish Market Blair at 7th has seating, though not upscale they have offerings ranging from Seafood Pizzas to Lobster tail.
PF Changs Coburg at Oakway (reservations recommended)
I also like Wings at the Eugene Airport, nice Chowder and ambience.
King Estate Winery would be another location for a memorable meal in the warmer months, especially, when you can sit on the patio and enjoy the view.
Ah, by the University.
The are lots of unique ethnic restaurants on 13th Ave right by Campus. In addition the Excelsior is there and that is the most upscale dining near campus. I love the Korean resaturant on Hillyard, across the street the the Dairy Queen.
On 14th between Alder and Hilyard is Pegas Pizza, nice local place, I love their smoked salmon Pizza.
Taylor's on 13th has some simple seafood entries on their menu, I know because we end up there before basketball games getting hydrated.
Enjoy your trip to Ducktown!!!
Sit down fish at the Fisherman's Market, on 6th (though it's not very close to the university). As mentioned above, besides Newman's and the Fisherman's Market, Eugene doesn't have any exclusively fish restaurants (I refuse to count McGraths!). Beppe and Gianni's, near the University, does some very nice things with baked fish sometimes.