Will the Seahawks wise up and run against the 49ers?

SANTA CLARA — The 49ers don’t come to mind when assessing the NFL’s top rushing defenses.

They’ve given ground at 4.3 yards per carry in an area where the term “stout” isn’t used until it gets below 4.0.

But the last two games, wins over Indianapolis and Chicago, came against teams that figured to challenge the 49ers at the line of scrimmage and impose their will. The Colts had Jonathan Taylor, the NFL’s No. 2 rusher with 1,559 yards. The Bears had one of the league’s top 1-2 punches with D’Andre Swift and Kyle Monangai, who have combined for 1,816 yards.

Neither team gashed the 49ers with the run, but mostly because they didn’t try. The Colts seemed intent on proving 44-year-old Philip Rivers could exploit the 49ers’ deficiencies defending the pass, and to an extent he succeeded until the game got out of hand. Taylor gained 47 yards on 16 carries.

The Bears averaged 5.0 yards per carry but only ran the ball 22 times. When faced with the 49ers’ porous secondary and minimal pass rush, Caleb Williams threw 42 passes (completing 25 for 330 yards) even though Chicago never trailed by more than seven points.

Instead of looking to control the line of scrimmage in the most basic way possible, both teams aired it out. The temptation to throw and throw again was too great and it contributed to a pace of play and style of game that benefitted the 49ers and coach Kyle Shanahan.

Now come the Seattle Seahawks (13-3), who will visit the 49ers (12-4) with the NFC West title, the No. 1 seed and a first-round bye on the line Saturday night at Levi’s Stadium.

Seattle, like Chicago, has its own 1-2 punch in Kenneth Walker III (930 yards on 205 carries, five touchdowns) and Zach Charbonnet (656 yards on 167 carries and 11 touchdowns. Seahawks offensive coordinator Klint Kubiak is the brother of 49ers offensive coordinator Klay Kubiak and was on Shanahan’s staff in 2023.

Will Klint Kubiak, under the direction of defensive-minded coach Mike Macdonald, be so tempted to throw against the 49ers that he abandons the run like Chicago did? He should be less inclined to be drawn into a score-for-score game based on his knowledge of how the 49ers operate.

Klint Kubiak is well-schooled in the Shanahan philosophy hoping to get 30 or more rushing plays in a game because it usually means controlling the gameplay, the clock and the outcome. Don’t be surprised if he uses that run discipline against the 49ers.

In the Seahawks’ 27-10 win over Carolina last week, they ran it 36 times for 163 yards. Charbonnet had a season-high 18 carries for 110 yards and two touchdowns and Walker 51 yards on 15 attempts. The week prior, Seattle had 171 yards on 25 carries including a 55-yard touchdown burst by Walker in a 38-37 win over the Los Angeles Rams.

In what could be wet and sloppy conditions, Seattle could come out looking to push the 49ers around. They’re on a roll with the run and there’s no proof the 49ers are capable of stopping it.

Defensive coordinator Robert Saleh likens Walker and Charbonnet to Chicago’s tandem.

“There is definitely different play styles, but two very effective backs,” Saleh said.”Charbonnet is probably more one-cut, where Kenneth can absolutely embarrass you running away from you.”

The 49ers have averaged 136 yards rushing per game over their six-game winning streak. The Seahawks have also gone in fits and starts with the run until the last two games.

“I think we’ve just stuck to our process and really believe what we’re doing,” Macdonald told reporters Wednesday. “Let’s go stick at it and iron this thing out and keep attacking it and hopefully it will come to life at some point. We’re still not there. Things aren’t going to go your way after a couple of weeks and all of a sudden you turn into a different type of team. That’s not the way to go.”

Sam Okuayinonu, a defensive end who is one of the 49ers’ better run defenders, said he won’t be too conscious of which back is in the game for Seattle even if their different styles might indicate plays which benefit either Walker or Charbonnet.

“It’s kind of hard to look at a game like that,” Okuayinonu said. “They’ve got two different backs, but you’ve got to set an edge and next up and make a play regardless of who is back there. I think that’s what it really comes down to, doing your assignment regardless of who is back there. Engage the offensive lineman, shut off the block and tackle him.”

Only two running backs have gained more than 100 yards against the 49ers this season: Jacksonville’s Travis Etienne (19 carries, 124 yards, one touchdown) and Tennessee’s Tony Pollard (104 yards on 14 carries). In a 20-10 win over Atlanta in their first game without middle linebacker Fred Warner, the 49ers held the Falcons’ Bijan Robinson to 40 yards on 14 carries.

But there have been instances of the 49ers giving too much ground and paying the price with losses. The Jaguars ran 32 times for 151 yards and beat the 49ers 26-21. Houston ran 36 times for 157 yards and won 26-15.

“Every time you take a run game away from a team and make it one-dimensional, it’s going to be pretty good for your team,” Okuayinonu said. “I’m pretty proud of the guys the way we’ve been handling these last few weeks.”

The Seahawks could decide to muscle up on the 49ers Saturday night, with the No. 1 seed hanging in the balance.