The developer of Seaport Square on the South Boston Waterfront will submit final designs this fall for the first three buildings in a massive development that will include offices, stores, and hundreds of homes.

Yesterday, developer John B. Hynes III said he has hired architects to design a pair of 20-story residential towers on Seaport Boulevard near the federal courthouse, plus a one-story structure that will house an innovation center to spur collaboration between new companies in the district.

The 23-acre project would replace parking lots that occupy much of the buildable land on the waterfront, which is drawing interest from medical and technology companies looking to relocate.

The development is a joint venture of Hynes’s firm, Boston Global Investors, and Morgan Stanley Real Estate Funds.

“We find ourselves in the position of rolling out a substantial amount of activity at Seaport Square to begin satisfying the various components that will make up and enhance the innovation district,’’ Hynes said in a statement.

His comments came as Boston’s mayor, Thomas M. Menino, announced new initiatives to attract more venture capital-backed firms to the waterfront and to encourage them to develop buildings that can accommodate solar power.

The mayor did not identify any specific incentives to attract venture-backed firms, but his administration recently used a $12 million property tax break to help bring Vertex Pharmaceuticals Inc. to the Fan Pier development, across from Seaport Square.

Menino said he hopes businesses will be attracted in part by the opportunity to collaborate with their peers on new business.

“We know that million-dollar VC deals, billion-dollar development deals, and business hires routinely happen outside of the office in common spaces,’’ Menino said in a speech at Boston College’s Citizen Seminar.

“We will be one of the first cities in the world to have a public innovation center — a place that fosters this type of collaboration.’’

Hynes said the innovation center at Seaport Square will be designed by the Boston architecture firm Hacin + Associates Inc., which drafted plans for the nearby FP3 housing complex. The building will contain 12,000 square feet on a single story.

The residential towers, with 300,000 square feet, will be designed by Elkus Manfredi Architects.

Elkus Manfredi also helped design the adjacent Fan Pier development by Joseph Fallon and the new Liberty Wharf, a development of restaurants and offices farther down Northern Avenue.

A spokesman for Hynes said he has not selected a start date for construction, but hopes to proceed soon after submitting final design plans to city regulators in September.

Casey Ross Boston Globe June 2, 2011