[2]: 604  He had one son, William Clapham, Jr., who served as a lieutenant in the Third Battalion, Pennsylvania Regiment of Foot after it was formed in late March, 1756,[3]: 53 [4]: 47  and who was killed by two Panis slaves in June 1762.

In 1748, Clapham was sent as a company commander to defend Annapolis Royal as part of a New England reinforcement for Nova Scotia, where he served with Jedidiah Preble and Benjamin Goldthwait.

On 19 August 1749, Captain Clapham was in command at Canso, Nova Scotia, when Lieutenant Joseph Gorham and his party were attacked by Mi'kmaq[10] who took twenty prisoners and carried them off to Louisbourg.

The bounty of scalps was raised to £50 in 1750, motivating Clapham and Francis Bartelo to form new ranger companies to search the land around Halifax for Mi'kmaq.

Clapham relieved John Gorham in the Battle at St. Croix on 23 March 1750,[1]: 175  by arriving at Pisiguit with his company of rangers and two cannons, forcing the Mi'kmaq to withdraw.

The mill was located about six miles north of Harris' Ferry, probably five hundred feet east of the mouth of Fishing Creek, near its confluence with the Susquehanna River, in present-day Dauphin County.

[32]: 72  The mill was fortified with a simple stockade in January, 1756, and garrisoned with volunteer militia recruited by Thomas McKee, an Indian trader who operated a trading post nearby.

[35] In March 1757, Governor William Denny met with Lord Loudoun, Conrad Weiser, and Colonel Clapham and determined that Fort Hunter should be demolished.

Clapham and his men marched from Harris's Ferry (present-day Harrisburg, Pennsylvania), while 18 bateaux and canoes loaded with materials traveled down the Susquehanna River, arriving on 11 June to start construction.

[3]: 52–61 [30] Clapham picked a site near a large stand of pines which he planned to use for construction, close to a water-powered sawmill on Armstrong Creek.

In a June 11 letter to Governor Morris, Clapham noted that the site he chose for the fort was appropriate because of "...the vast Plenty of Pine Timber at Hand, its nearness to Shamokin and a Saw within a Quarter of a Mile."

Once finished, it was garrisoned by Pennsylvania Colonial Militia and served as the chief supply post between the area settlements and Shamokin where Fort Augusta would be built later that summer.

[43] In June, 1756, Major James Burd finally received sufficient funding and supplies to begin building Fort Augusta at the former site of the Native American village of Shamokin.

[33] The fort was positioned so as to prevent Native American war parties from descending the Susquehanna River, to serve as a refuge for civilians under attack, and as a staging area for military expeditions against enemy forces.

[44]: 180  The plan of the fort had been previously drawn up by Governor Morris, who wrote to Clapham on 12 June recommending "a square with one ravelin to protect the curtain where the gate is, with a ditch, covered way, and glacis.

"[3]: 54  In early July, Clapham marched with his troops from Fort Halifax, while the canoes and bateaux carried supplies downriver, encountering numerous falls and rapids which hindered their progress.

[3]: 55 [45] On 14 August, Clapham wrote to Governor Morris: "We have the walls of the fort now above-half finished and our other works in such situation that we can make a very good defense against any body of French and Indians that shall seat themselves before us without cannon.

[29]: 488  Named for Augusta of Saxe-Gotha, the mother of King George III, it was the largest British fort built in Pennsylvania, with earthen walls more than two hundred feet long topped by wooden fortifications.

On 7 September 1756, he wrote to Franklin requesting permission to hire another carpenter for additional fortification of the fort's walls: On 8 September 1756, he wrote to Franklin requesting additional supplies and horses: In late October, Clapham described the final stages of the fort's construction: "In eight or ten days more the ditch will be carried quite around the parapet, the barrier gates finished and erected, and the pickets of the glacis completed.

[53][32]: 72 [33] In November 1756, Clapham informed Deputy Governor William Denny that about fifty miles up the West Branch Susquehanna River was an Indian village with only ten families, located near Great Island (now known as Lock Haven, Pennsylvania).

He ordered a raiding party of 42 men, with Andrew Montour acting as a guide, to destroy the village,[42]: 573 [54]: 285, 394  and instructed the commander, Captain Hambright, "to Kill, Scalp, and capture as many as you can."

[61]: 148 Soon afterwards, Clapham entered into an economic venture with Indian trader George Croghan to develop a trading post and a settlement, later referred to as Oswegly Old Town.

[62][63] In 1762, he applied for the right to settle on land 18 miles southeast of Fort Pitt, which he had purchased from George Croghan, and his application was approved by Colonel Bouquet and General Robert Monckton.