Sweden wanted a bridge, Denmark wanted a tunnel, they compromised

Why wouldnt they just make whole thing a tunnel

Good question. I think, and I don't know shit about bridges and tunnels, but I think the tunnel is probably more expensive. Part of the passage had to be tunnel so they did as much tunnel as they needed and did the rest as a bridge since that was cheaper.

From wikipedia: "The justification for the additional expenditure and complexity related to digging a tunnel for part of the way, rather than raising that section of the bridge, was to avoid interfering with air traffic from the nearby Copenhagen Airport, to provide a clear channel for ships in good weather or bad, and to prevent ice floes from blocking the strait."